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Laboratory for Omix Technologies and big data for Personalized Medicine and Health

Invited researcher Borchers Christoph Hermann
Contract number
075-10-2019-083
Time span of the project
2019-2021

As of 15.02.2021

17
Number of staff members
12
scientific publications
1
Objects of intellectual property
General information

Name of the project: Next generation proteomics for enhancement of personalized medicine and healthcare

Strategy for Scientific and Technological Development Priority Level: в

Goals and objectives

Project objective: Development of a modern, reliable, precise, rapid and affordable method for quantitative evaluation of human proteome and its implementation into clinical practices for objectivization of criteria in personalized medicine

The practical value of the study

Pursuing the main goal of the project of developing novel mass spectrometry (MS)-based proteomics analytical technologies for biomedical research and clinical implication, we are generating protein-biomarker assessment assays for quantitation of 1000 proteins in one sample of human blood plasma with utilization of new type of mass spectrometer (timsTOF Pro) with the ion mobility option and parallel reaction monitoring (PRM) mode, which cumulatively provides unequaled specificity, reproducibility, multiplexing capability, analytical throughput and sensitivity compared with current MS methods.

The optimization of liquid chromatography (LC)-MS conditions for PRM mode on timsTOF Pro mass spectrometer for near 300 proteins was completed and compared with MRM-based data obtained on currently used QQQ MS instruments. We demonstrated that new generation timsTOF Pro mass spectrometer in PRM mode can be effectively used for targeted absolute quantitative proteomics with a high level of specificity and sensitivity. The established in the laboratory high-throughput synthesis of peptide standards, which are a key part of the technology, is efficiently providing the extension of the technology development range to 1000 proteins in one sample.

The quantitation of 270 clinically significant proteins of blood plasma from healthy volunteers has been performed to establish the regional normal range, which has been previously shown before depends from population ethnic background.

We have developed and tested method of detection of SARS CoV-2 virus in epithelial smears from the nasopharynx, based on mass spectrometry detection of the virus’s N protein. The method allows reliable detection the virus even in patients with low viral load. The result was published in Q1 journal (Journal of Proteome Research) and submitted patent application is approved.

Several conducted and published studies support the concept of the implementation of MS-based proteomic technologies into clinical practice specifically precision oncology.

Implemented results of research:

The assay of mass spectrometry viral protein based detection of SARS-CoV-2 is testing in V. I. Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Moscow (Russia). 

Education and career development:

  • The 162 hours, 6 credits “Omics Technologies” course for Master and PhD Skoltech students of «Life Sciences» and «Computational and Data Science and Engineering programs» has been created and implemented.
  • The 81 hours, 3 credits “Postgenomic Technologies for Precision Medicine” course for the same audience has been created and included to Skoltech education program.
  • 3 PhD students and 3 Master students in the laboratory.
  • Had 1 PhD defense and 1 PhD defense is planning.   

Organizational and structural changes:

  • Peptide synthesis group (established).
  • Skoltech Project Center: Mass Spectrometry and Omics Technologies (under establishment).   
  • MRM Proteomics R, LLC (established) – Skoltech spin-off company for commercialization of the laboratory developments.  

Collaborations:

  • McGill University, Department of Oncology & Segal Cancer Proteomics Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, (Canada): R&D collaboration.
  • Bruker Daltonics (Germany): R&D collaboration.
  • V.N. Orekhovich Research Institute of Biomedical Chemistry (Russia): R&D collaboration.
  • V. I. Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation (Russia): R&D collaboration.
  • Institute of Biomedical Problems-Russian Federation State Scientific Research Center, Russian Academy of Sciences (Russia): R&D collaboration.


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Kashirina DN, Brzhozovskiy AG, Pastushkova LK, Kononikhin AS, Borchers CH, Nikolaev EN, Larina IM.
Semiquantitative Proteomic Research of Protein Plasma Profile of Volunteers in 21-Day Head-Down Bed Rest. Front Physiol. 2020 Jul 24;11:678. – Q1.
Nikolaev EN, Indeykina MI, Brzhozovskiy AG, Bugrova AE, Kononikhin AS, Starodubtseva NL, Petrotchenko EV, Kovalev GI, Borchers CH, Sukhikh GT
Mass-Spectrometric Detection of SARS-CoV-2 Virus in Scrapings of the Epithelium of the Nasopharynx of Infected Patients via Nucleocapsid N Protein. J Proteome Res. 2020 Nov 6;19(11):4393-4397. – Q1.
Ibrahim S, Froehlich BC, Aguilar-Mahecha A, Aloyz R, Poetz O, Basik M, Batist G, Zahedi RP, Borchers CH.
Using Two Peptide Isotopologues as Internal Standards for the Streamlined Quantification of Low-Abundance Proteins by Immuno
Richard VR, Zahedi RP, Eintracht S, Borchers CH.
An LC-MRM assay for the quantification of metanephrines from dried blood spots for the diagnosis of pheochromocytomas and paragangliomas. Anal Chim Acta. 2020 Sep 1;1128:140-148. – Q1.
Michaud SA, Pětrošová H, Jackson AM, McGuire JC, Sinclair NJ, Ganguly M, Flenniken AM, Nutter LMJ, McKerlie C, Schibli D, Smith D, Borchers CH.
Process and Workflow for Preparation of Disparate Mouse Tissues for Proteomic Analysis. J Proteome Res. 2021 Jan 1;20(1):305-316. – Q1.
Froehlich BC, Popp R, Sobsey CA, Ibrahim S, LeBlanc AM, Mohammed Y, Aguilar-Mahecha A, Poetz O, Chen MX, Spatz A, Basik M, Batist G, Zahedi RP, Borchers CH.
Systematic Optimization of the iMALDI Workflow for the Robust and Straightforward Quantification of Signaling Proteins in Cancer Cells. Proteomics Clin Appl. 2020 Sep;14(5):e2000034. – Q3 (WoS), Q2 (Scopus).
Gaspar VP, Ibrahim S, Sobsey CA, Richard VR, Spatz A, Zahedi RP, Borchers CH.
Direct and Precise Measurement of Bevacizumab Levels in Human Plasma Based on Controlled Methionine Oxidation and Multiple Reaction Monitoring. ACS Pharmacol Transl Sci. 2020 Nov 13;3(6):1304-1309. IF and Q for 2019 is calculating.
Bhowmick P, Roome S, Borchers CH, Goodlett DR, Mohammed Y.
An Update on MRMAssayDB: A Comprehensive Resource for Targeted Proteomics Assays in the Community. J Proteome Res. 2021 Apr 2;20(4):2105-2115. – Q1
Li FKK, Gale RT, Petrotchenko EV, Borchers CH, Brown ED, Strynadka NCJ.
Crystallographic analysis of TarI and TarJ, a cytidylyltransferase and reductase pair for CDP-ribitol synthesis in Staphylococcus aureus wall teichoic acid biogenesis. J Struct Biol. 2021 Apr 2;213(2):107733. – Q1
Mohammed Y, Bhowmick P, Michaud SA, Sickmann A, Borchers CH.
Mouse Quantitative Proteomics Knowledgebase: reference protein concentration ranges in 20 mouse tissues using 5000 quantitative proteomics assays. Bioinformatics. 2021 Jan 23:btab018. doi: 10.1093/bioinformatics/btab018. Epub ahead of print. PMID: 33483739. – Q1
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